To remap the seach button to something instead of search, put something along the lines of the following into ~/.xbindkeysrc
Example here is to remap it to alt+f4 to close a window.

"/usr/bin/xvkbd -text "\[Alt_L]\[F4]""
c:0xE1

Alternatively, Gnome will recognize the small middle search button as a keyboard event. Thus, you just have to go into keyboard shortcuts and remap that to something. This is probably the most reliable way to go about using this key.

It is possible to use xmodmap to register the button press as a middle click. Begin by assigning the key event to Pointer_Button 2.

echo "keycode 225 = Pointer_Button2" >> ~/.xmodmaprc

Now, just create a startup script that feeds that input into xmodmap when your window manager starts. In KDE4 create ~/.kde4/Autostart/middleclick with the following contents.

#!/bin/sh
xmodmap ~/.xmodmaprc

And don't forget to give it execute permissions.

chmod +x ~/.kde4/Autostart/middleclick

The trick only works when "mousekeys" are on. So either gnome-keyboard-properties -> Mousekeys -> Enable pointer OR toggle with SHIFT-ALT-NUMLOCK (you want to be able to toggle so you can use the numeric keypad at times). Or in KDE System Settings -> Keyboard & Mouse -> Mouse -> Mouse Navigation -> Check "Move pointer with keyboard (using the num pad)"

Lastly, add xbindkeys to your startup and you should be good to go.

Mouse Wheel Mode

In order to enable or disable mouse wheel's free spinning, you can use revoco. Giving the following command from shell, or, alternatively, putting it in a script executed at the startup should enable/disable free spinning.

revoco free # in order to enable free spinning
revoco click # in order to disable free spinning